LXL04_037789 | RubberDandelionOmics

Gene overview

LXL04_037789

Reference: OH-1004 Chr: Chr09 Coordinates: 21211371-21212567 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1197 bp · LXL04_037789|LXL04_037789|OH1004|cDNA

ATGTTATCGCCACTGCCGTTGCCGGAGATTGTCATCACAGCGTCGCCTGATGGTCCGTTCACCGCCTACGATCCAAACTCTGGAAGTGTGGTAGGTCGGTTTAATGGCAACCGGTGTCCTCGTAACGGCATCTGTGTTCTCGGAAAAGAGCTATTCGCCGCTTCACATGTTTCGCCGGAGACACGTGCAGGCTATGTTCGTATCTATTACTGGTGGTCGATGTCACGTGTGAAGAGTATTCCTCTCCCTGAACCTGTAGC...

CDS

Download CDS FASTA

1197 bp · LXL04_037789|LXL04_037789|OH1004|CDS

ATGTTATCGCCACTGCCGTTGCCGGAGATTGTCATCACAGCGTCGCCTGATGGTCCGTTCACCGCCTACGATCCAAACTCTGGAAGTGTGGTAGGTCGGTTTAATGGCAACCGGTGTCCTCGTAACGGCATCTGTGTTCTCGGAAAAGAGCTATTCGCCGCTTCACATGTTTCGCCGGAGACACGTGCAGGCTATGTTCGTATCTATTACTGGTGGTCGATGTCACGTGTGAAGAGTATTCCTCTCCCTGAACCTGTAGC...

Protein

Download Protein FASTA

398 aa · LXL04_037789|LXL04_037789|OH1004|PROTEIN

MLSPLPLPEIVITASPDGPFTAYDPNSGSVVGRFNGNRCPRNGICVLGKELFAASHVSPETRAGYVRIYYWWSMSRVKSIPLPEPVAPLAGSVDGLYVFSGGISGQIHSVSVHSGDVIRSFPVHEKPVSCVTINRDGSLILSGSDDGTIAVLPILLLLDISVDMESRYSSFTRFTGHESSVTGLTAGMGRRGGIMISSSLDCTCKMWSLNGIHLQTVRFPVEVWCTALNPPETELFAAGIDGMVYKRRLMVERRKQFLEG...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_037789`
TK1151 ID	TkA04G351220
OH-1004 ID	LXL04_037789
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_037789

Location Chr09:21211371-21212567 (+)

Description Similar to RID3: Protein ROOT INITIATION DEFECTIVE 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g49180`	Involved in meristem development.	Identification of novel meristem factors involved in shoot regeneration through the analysis of temperature-sensitive mutants of Arabidopsis.2009 · DOI: 10.1111/j.1365-313x.2008.03750.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_037789 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0006261 DNA-templated DNA replication Biological Process

GO:0006364 rRNA processing Biological Process

GO:0007368 determination of left/right symmetry Biological Process

GO:1902184 negative regulation of shoot apical meristem development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005656 nuclear pre-replicative complex Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0080008 Cul4-RING E3 ubiquitin ligase complex Cellular Component

GO:0120293 dynein axonemal particle Cellular Component

KEGG gene cross-reference

ath:AT3G49180

bta:533356

dre:445819

hsa:57418

xla:733228

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.935

Rank 1 · LXL04_037789 · OH-1004

Cytoplasm0.115

Rank 2 · LXL04_037789 · OH-1004

Cell membrane0.019

Rank 3 · LXL04_037789 · OH-1004

Mitochondrion0.014

Rank 4 · LXL04_037789 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_037789 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF25174.2Beta-prop_THOC365-213 aa

PF23414.2Beta-prop_EML_265-209 aa

PF24817.2WD40_WDHD1_1st66-210 aa

PF25172.2Beta-prop_WDR3_2nd66-210 aa

PF25173.2Beta-prop_WDR3_1st86-242 aa

PF23381.2Beta-prop_IFT122_1st92-305 aa

PF25047.1Beta-prop_TEP1_2nd92-243 aa

PF24807.2WD40_CDC20-Fz92-212 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037789	`PF25174.2`	Beta-prop_THOC3	65	213	1.4e-11	44.6
LXL04_037789	`PF23414.2`	Beta-prop_EML_2	65	209	3.1e-11	43.9
LXL04_037789	`PF24817.2`	WD40_WDHD1_1st	66	210	3.4e-11	43.6
LXL04_037789	`PF25172.2`	Beta-prop_WDR3_2nd	66	210	2.5e-08	34.2
LXL04_037789	`PF25173.2`	Beta-prop_WDR3_1st	86	242	1.4e-18	68.0
LXL04_037789	`PF23381.2`	Beta-prop_IFT122_1st	92	305	6.7e-14	52.6
LXL04_037789	`PF25047.1`	Beta-prop_TEP1_2nd	92	243	3.2e-11	43.6
LXL04_037789	`PF24807.2`	WD40_CDC20-Fz	92	212	1e-08	35.6
LXL04_037789	`PF25175.2`	Beta-prop_WDR5	95	151	2.2e-17	64.0
LXL04_037789	`PF24814.2`	WD40_Prp19	96	210	2.7e-12	47.0
LXL04_037789	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	98	229	7.2e-10	39.4
LXL04_037789	`PF20426.5`	NBCH_WD40	100	154	1e-09	38.5
LXL04_037789	`PF23411.2`	Beta-prop_Vps41	101	153	5.4e-06	26.6
LXL04_037789	`PF00400.39`	WD40	116	150	2.5e-18	66.4
LXL04_037789	`PF24805.2`	EIF3I	124	307	8.9e-08	32.3

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9M3B4`	Arabidopsis thaliana	Protein ROOT INITIATION DEFECTIVE 3	30.263%	Swiss-Prot	moderate database homology

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